Status
Assembly v2 (May 2013) is an improved draft assembly. 1299 scaffolds and 52.6 Mbp were assembled by AllPathsLG using Illumina gDNAs and then patched by PBJelly using PacBio gDNAs.
Summary statistics for the Laccaria amethystina LaAM-08-1
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 52.58 |
| Sequencing read coverage depth | 156.5x |
| # of contigs | 1999 |
| # of scaffolds | 1299 |
| # of scaffolds >= 2Kbp | 1034 |
| Scaffold N50 | 112 |
| Scaffold L50 (Mbp) | 0.12 |
| # of gaps | 700 |
| % of scaffold length in gaps | 1.9% |
| Three largest Scaffolds (Mbp) | 0.84, 0.70, 0.66 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | JGI_RNA_contigs | 31231 | 29635 | 94.9% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1517 | 1230 |
| transcript | 1238 | 986 |
| exon | 242 | 150 |
| intron | 70 | 56 |
| description: | ||
| protein length (aa) | 364 | 278 |
| exons per gene | 5.12 | 4 |
| # of gene models | 17553 |
Collaborators
- DOE Joint Genome Institute
- Francis Martin at MycorWeb
- Annegret Kohler at MycorWeb.
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canbäck B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Doré J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Högberg N, Johansson T, Khouja HR, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Tunlid A, Grigoriev IV, Hibbett DS, Martin F
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
Nat Genet. 2015 Apr;47(4):410-5. doi: 10.1038/ng.3223
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canbäck B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Doré J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Högberg N, Johansson T, Khouja HR, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Tunlid A, Grigoriev IV, Hibbett DS, Martin F
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
Nat Genet. 2015 Apr;47(4):410-5. doi: 10.1038/ng.3223
Funding
The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
